In Rethymnon there is the University of Crete offering year round courses in Modern Greek, both winter and (intensive) summer.
Also, there is a private language school in Chania - Lexis in ?Daskalogiannis St. if I recall correctly.
Further afield but judging from its excellent quality textbooks Taksidi Stin Ellada - three volumes. levels A1/A2, B1/B2, C1/C2 - is the University of Athens courses, again year round and intensive summer beginning June into July.